wrong consensus sequence from hhmake

[antoineszatkownik]

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Expected Behavior

consensus sequence should look like this : LHCCGVTNYrDWxDTNYYSEKGFPKSCCKLEdxxCxPQRDxxxxxxxADKVNNE

Current Behavior

consensus sequence made by hhmake look like this : LxCCGvxnyxdWxxTxYyxexGxPkSCCxxxxxxxxxdxxkVxxe

Steps to Reproduce (for bugs)

the hhmake command line is the following : hhmake ./msa_s_exon_2_0.a2m -o ./msa_s_exon_2_0.hhm -v 0 -name ENSG00000000003#2_0 -id 100.0 -M a2m -qsc 0

Context

I've tried this hhmake command with several parameters values and in .fasta format (with M=50 no qsc) with .a2m and no qsc or different qsc values.

In .fasta format it just choose the first sequence in the query MSA as consensus

Your Environment

Include as many relevant details about the environment you experienced the issue in.

• Version/Git commit used: hhsuite-osx-universal.tar.gz 08-Jul-2021 14:22 and also tried with hhsuite-3.3.0-SSE2-Linux.tar.gz
• Operating system and version: macOS Monterey 12.1, Mac M1 8Go